The trial, which began in 1966 at the federal courthouse of Meridian before an all-white jury,[12] convicted seven conspirators, including the deputy sheriff, and acquitted eight others. It was the first time a white jury convicted a white official of civil rights killings.[13] For three men, including Killen, the trial ended in a hung jury, with the jurors deadlocked 11–1 in favor of conviction. The lone holdout said that she could not convict a preacher. The prosecution decided not to retry Killen and he was released. None of the men found guilty would serve more than six years in prison.[14]

More than 20 years later, Jerry Mitchell, an award-winning investigative reporter for The Clarion-Ledger in Jackson, Mississippi, wrote extensively about the case for six years. Mitchell helped to secure convictions in other high-profile Civil Rights Era murder cases, including the assassination of Medgar Evers, the 16th Street Baptist Church bombing, and the murder of Vernon Dahmer. Mitchell assembled new evidence regarding the murders of the three civil rights workers. He also located new witnesses and pressured the state to take action. Assisting Mitchell were high school teacher Barry Bradford and a team of three students from Illinois.[15]

The students persuaded Killen to do his only taped interview (to that point) about the murders. That tape showed Killen clinging to his segregationist views and competent and aware. The student-teacher team found more potential witnesses, created a website, lobbied the United States Congress, and focused national media attention on reopening the case. Carolyn Goodman, the mother of one of the victims, called them "super heroes".[15]

In 2004, Killen declared that he would attend a petition-drive on his behalf, which was to be conducted by the Nationalist Movement at the 2004 Mississippi Annual State Fair in Jackson. The Nationalist Movement opposed communism, integration and non-speedy trials. The Hinds County sheriff, Malcolm MacMillan, conducted a counter-petition, calling for a reopening of the state case against Killen. Killen was arrested for three counts of murder on January 6, 2005. He was freed on bond. His case drew comparisons to that of Byron De La Beckwith, who was charged with the killing of Medgar Evers in 1963 and rearrested in 1994.[citation needed]

Killen's trial was scheduled for April 18, 2005. It was deferred after the 80-year-old Killen broke both of his legs while chopping lumber at his rural home in Neshoba County. The trial began on June 13, 2005, with Killen attending in a wheelchair. He was found guilty of manslaughter on June 21, 2005, 41 years to the day after the crime. The jury, consisting of nine white jurors and three black jurors, rejected the charges of murder, but found him guilty of recruiting the mob that carried out the killings. He was sentenced on June 23, 2005, by Circuit Judge Marcus Gordon to the maximum sentence of 60 years in prison, 20 years for each count of manslaughter, to be served consecutively.[7] He would have been eligible for parole after serving at least 20 years. At the sentencing, Gordon stated that each life lost was valuable, and he said that the law made no distinction of age for the crime and that the maximum sentence should be imposed regardless of Killen's age. Prosecuting the case were Mississippi Attorney GeneralJim Hood and Neshoba County District Attorney Mark Duncan.[citation needed]

On August 12, Killen was released from prison on a $600,000 appeal bond. He claimed that he could no longer use his right hand (using his left hand to place his right one on the Bible during his swearing-in) and that he was permanently confined to his wheelchair. Gordon said he was convinced by the testimony that Killen was neither a flight risk nor a danger to the community. On September 3, The Clarion-Ledger reported that a deputy sheriff saw Killen walking around "with no problem". At a hearing on September 9, several other deputies testified to seeing Killen driving in various locations. One deputy said that Killen shook hands with him using his right hand. Gordon revoked the bond and ordered Killen back to prison, saying that he believed Killen had committed a fraud against the court.[16]

On March 29, 2006, Killen was moved from his prison cell to a City of Jackson hospital to treat complications from the severe leg injury that he sustained in the 2005 logging incident. On August 12, 2007, the Supreme Court of Mississippi affirmed Killen's conviction by a vote of 8–0 (one judge not participating).[17]

On February 25, 2010, the Associated Press reported that Killen filed a lawsuit against the FBI.[20] The suit alleged that one of Killen's lawyers in his 1967 trial, Clayton Lewis, was an FBI informant, and that the FBI hired "gangster and killer" Gregory Scarpa to coerce witnesses.[20] On February 18, 2011 U.S. Magistrate F. Keith Ball recommended that the lawsuit be dismissed. On March 23, 2011, District Judge Daniel P. Jordan, III, adopted the magistrate's report and dismissed the case.

James Hart Stern, a black preacher from California, shared a prison cell with Edgar Ray Killen from August 2010 to November 2011. During that time, Killen and Stern forged a close relationship and Killen hand wrote dozens of letters to Stern outlining his views on race as well as confessing to other crimes. In addition to the letters, the former leader of the KKK signed over power of attorney and his land in Mississippi to his cellmate.[21] Stern detailed his experience in the 2017 book Killen the KKK, co-authored by North Carolina author Autumn K. Robinson. Using his power of attorney, Rev. Stern disbanded Killen's incarnation of the KKK on January 5, 2016.[22]

On January 12, 2018, it was announced that he had died at the age of 92 at the Mississippi State Penitentiary in Parchman, Mississippi.[7][23]

^The Civil Rights Act of 1968, passed in part due to this case, provided for life imprisonment or the death penalty for deprivations of civil rights resulting in bodily injury or death. Prior to that, the maximum penalty was ten years.